Agricultural losses due to plant pathogen infestations are estimated at $40 billion annually in the U.S. alone. Advanced disease detection and prevention in crops is a challenge for sustainable agriculture. Among the various types of pathogens that attack crops, fungi are the most common and most devastating for crops from Michigan to Florida in the east coast to California, Arizona and Mexico in the west. Pathogenic fungal infections cause numerous diseases such as white mold, grey mold, crown rot, leaf blight, fruit rot etc. in a variety of grain, fruit, and vegetable crops. For example, Phytophthora capsici alone is known to infect as many as 68 crops from 27 different families across the U.S.
The infections occur at multiple sites in crops (e.g., root, leaf, stem, fruit) during growth or after harvest, such as when produce is being stored or transported. If not controlled early, these infections spread quickly by wind, water, or physical contact between plants, causing devastating economic loss. The narrow profit margin greatly limits producers' options for effective controls for these diseases. Economic management of fruits may be challenging, as fruits are exposed to fungal inoculum for an extended period of time. Due to the lack of early-detection technology, fungicide application (even multiple applications) may come late and prove ineffective, resulting in almost 90% grower losses in some cases. Frequently these crops are sold through mass distribution well before the infections are known. Therefore, an early detection of pathogen infections could help growers contain the infection, spray only when needed, and minimize economical losses.
Currently used methods for disease detection in agricultural crops include direct methods, such as pathogen isolation and identification based on morphological characteristics, polymerase chain reaction (PCR), fluorescence in-situ hybridization (FISH), immunofluorescence (IF), enzyme-linked immuno-sorbent assay (ELISA), and gas chromatography mass spectrometry (GC-MS). There are also indirect methods, such as hyper spectral imaging, fluorescence, and other spectroscopy based techniques. These methods are time consuming, destructive, demand skilled analysts, require a laboratory set-up, and, unfortunately, do not offer either real-time monitoring or on-field deployment possibilities. Due to their destructive nature, direct methods can only be employed after the onset of disease symptoms to verify the infection, and thus do not allow for early monitoring and prevention. The indirect methods are expensive, do not possess high selectivity towards the infection/disease, and are primarily effective for post-harvest evaluation.